Dr. Thomas C. Bishop
Center for Bioenvironmental Research
Tulane and Xavier Universities
New Orleans, LA

Monday, October 18, 2004
3:00 pm (CT)
3269 Beckman Institute

Abstract

Nucleosomes organize the folding of DNA into chromatin in all eukaryotic cells and significantly influence transcription, replication, regulation and repair. Molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution have been conducted. DNA helical parameters (Roll, Tilt, Twist, Shift, Slide, Rise) were extracted from each trajectory to compare the conformation, effective force constants, persistence length measures, and fluctuations of nucleosomal and free DNA. Results indicate: 1) the superhelical path of DNA in the nucleosome is irregular at the basepair level and has 20% more bend near the dyad, 2) the free DNA achieves enough bend and shear in solution to create an ideal nucleosome superhelix and exhibits a long wavelength (~44Å) structural variation that may affect nucleosome asymmetry, 3) DNA is less flexible in the nucleosome than when free in solution, and 4) the power spectra of the fluctuations of helical parameters as functions of basepair distance tend towards longer wavelengths in the nucleosome than free DNA. Results are discussed in relation to the theory of elastic rods and experimental observations.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.